GetSampleDEFun: Sample-specific differentially expressed (DE) genes

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Sample-specific differentially expressed (DE) genes

Description

This function computes the median expression of a gene across all samples and further computed the fold change of that gene to the computed median expression. A gene was considered up if the fold-change ≥ 4 and down if the fold-change ≤ −4.

Usage

GetSampleDEFun(
  RnaSeq_data,
  parallel = c("TRUE", "FALSE"),
  ncores = 2,
  CTDDirectory = "~"
)

Arguments

RnaSeq_data	A R dataframe with gene-centric expression values of bulk tumor samples. Rows are the genes, columns are the tumor samples.
parallel	A boolean value ('TRUE' or 'FALSE')indicating if the users want to run this function in multi-core.
ncores	An integer value for the number of cores.
CTDDirectory	A character string for the file path of the directory for the output to be stored.

Details

Created By: Banabithi Bose| Date Created: 4/10/2022 | Stage 3 | Function 1 |

Value

R dataframe objects each with a single column containing DE genes for each tumor sample. The column is labeled as gene.

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.